LTPDB - the non-specific Lipid Transfer Protein Database for Plant

Welcome to the LTPDB

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Lipids are hydrocarbons insoluble in water but soluble in organic solvents. They are commonly translocated among subcellular membranes to enable various metabolic activities. Lipid transfer proteins (LTPs) have been found in animals, plants and some fungi, and they exist in many tissues with various sizes and functions.(Kader, J. C. 1996)

LTPs play an important role not only in plant but also in human.It mediates in vitro the transfer of all common phospholipids, cholesterol and gangliosides between membranes. The term plant "nonspecific lipid transfer proteins" indicates that LTPs can associate with various phospholipids with broad specificity. The first known plant lipid transfer protein was isolated from potato tuber in 1975 by Kadar. At present, much more nsLTPs have been found in monocots, dicots and gymnosperms. etc. Plant nsLTPs are a kind of small (usually 6.5 to 10.5 kDa), basic (isoelectric point, or pI, usually falls between 8.5 and 12) and stable (with four conserved disulfide bonds) proteins. (Kader, J.C. 1993)

NsLTPs are stabilized by eight conserved cysteine forming four disulfide bonds and they usually contain signal peptides in the N-terminus1. Previous studies showed that nsLTPs can be divided into two main groups according to their molecular weight: nsLTP1 (9 kDa) and nsLTP2 (7 kDa)16. These two groups exhibit different disulfide bond patterns.The disulfide bond linkages of nsLTP1 at Cys1-Cys6 and Cys5-Cys8 differ from those of nsLTP2 at Cys1-Cys5 and Cys6-Cys8. The major difference is observed at C6-X-C8 motif. For the CXC motif in nsLTP1, the residue X is a hydrophilic residue, for example asparagines; however, in nsLTP2, a hydrophobic residue, such as leucine or phenylalanine, was found at the X position. These conserved hydrophilic or hydrophobic residues may play important roles in the biological functions of nsLTPs. (Odani, S. 1989)

Plant non-specific lipid transfer proteins are one of the most well-known proteins that are widely distributed in the plant kingdom. Our wet-lab laboratory has been studying nsLTPs for years , but there is still much unknown space left about these sequence highly-diverse proteins. Importantly, there is no nsLTPs database systematically collecting and organizing relevant data about nsLTPs.

Boutrot et al, 2008. had identified and classified 267 nsLTPs sequences in 2008, but their method still failed to classify many nsLTPs. We aimed to establish an nsLTPs database, develop a robust classification method for nsLTPs and formulate a Prosite signature patterns for the identification of nsLTPs as well as the key residues for the structural stability or in the lipid binding ability of nsLTPs.

The nsLTPDB provides some informations for studying Plant and Lipid Transfer Protein relationships. This site also offers some analysis results like Phylogenetic tree and Multiple sequence alignment in order to offer some information in academic researches and biotechnological developments.

 

Methods

Primary data of nsLTPDB were collected from the National Center for Biotechnology Information (NCBI) and related plant database by using program and visual inspections were then performed to refine the data.

 

Statistics

The non - specific Lipid Transfer Protein subset of nsLTPDB contains about 121 species.

 

Classification

 

Our Lab's References

Liu YJ, Samuel D, Lin CH, Lyu PC.: Purification and characterization of a novel 7-kDa non-specific lipid transfer protein-2 from rice (Oryza sativa).Biochem Biophys Res Commun 2002, Jun 14;294(3):535-40. [Abstract] [PDF]

Samuel D, Liu YJ, Cheng CS, Lyu PC.: Solution structure of plant nonspecific lipid transfer protein-2 from rice (Oryza sativa). J Biol Chem. 2002 Sep 20;277(38):35267-73. [Abstract] [PDF]

Cheng HC, Cheng PT, Peng P, Lyu PC, Sun YJ.: Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa. Protein Sci. 2004 Sep;13(9):2304-15. Epub 2004 Aug 4.[Abstract] [PDF]

Cheng CS, Samuel D, Liu YJ, Shyu JC, Lai SM, Lin KF, Lyu PC.:Binding mechanism of nonspecific lipid transfer proteins and their role in plant defense.Biochemistry. 2004 Nov 2;43(43):13628-36.[Abstract] [PDF]

Lin KF, Liu YN, Hsu ST, Samuel D, Cheng CS, Bonvin AM, Lyu PC.: Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean. Biochemistry. 2005 Apr 19;44(15):5703-12., 58:618-627.[Abstract] [PDF]

Cheng CS, Chen MN, Lai YT, Chen T, Lin KF, Liu YJ, Lyu PC.:Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding.Proteins. 2008 Feb 15;70(3):695-706.[Abstract] [PDF]

Lai YT, Cheng CS, Liu YN, Liu YJ, Lyu PC.:Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: a model from molecular simulations. Proteins. 2008 Sep;72(4):1189-98.[Abstract] [PDF]

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